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Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps

Bahareh Behkamal, Mahmoud Naghibzadeh, Mohammad Reza Saberi, Zeinab Amiri Tehranizadeh, Andrea Pagnani, Kamal Al Nasr
2021 Biomolecules  
Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem.  ...  Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching  ...  Afterward, the 3D vector matching problem is transformed into the 3D graph matching problem based on the extracted features. The construction of the graph is elaborated in the following.  ... 
doi:10.3390/biom11121773 pmid:34944417 pmcid:PMC8698881 fatcat:rgc4gstccfetnjgadloxewpqey

Sex in graphs

Oystein Ore
1960 Proceedings of the American Mathematical Society  
The problem. The present study in graph theory is inspired by a problem arising in the field of biology.  ...  Its connected components are the sets V*(a). 6. The dichotomy problem. We shall now return to the biological graph problem introduced in §1.  ... 
doi:10.1090/s0002-9939-1960-0117174-7 fatcat:o7vnikgwpvfdxfjgzoai4li72m

Sex in Graphs

Oystein Ore
1960 Proceedings of the American Mathematical Society  
The problem. The present study in graph theory is inspired by a problem arising in the field of biology.  ...  Its connected components are the sets V*(a). 6. The dichotomy problem. We shall now return to the biological graph problem introduced in §1.  ... 
doi:10.2307/2034706 fatcat:4euls3ejanbvtgv5meb6bt3pt4

Memetic Algorithms for the MinLA Problem [chapter]

Eduardo Rodriguez-Tello, Jin-Kao Hao, Jose Torres-Jimenez
2006 Lecture Notes in Computer Science  
This paper presents a new Memetic Algorithm designed to compute near optimal solutions for the MinLA problem.  ...  Its performance is investigated through extensive experimentation over well known benchmarks and compared with other state-of-the-art algorithms.  ...  The authors would like to thank Andrew J. McAllister who has kindly provided us with his source code. The reviewers of the paper are greatly acknowledged for their constructive comments.  ... 
doi:10.1007/11740698_7 fatcat:7q2ddbttyvfqlkkxgapp3gsijm

Decomposing Matrices into Blocks

Ralf Borndörfer, Carlos E. Ferreira, Alexander Martin
1998 SIAM Journal on Optimization  
More precisely, given some matrix A, we try to assign as many rows as possible to some number ß of blocks of size K such that no two rows assigned to different blocks intersect in a common column.  ...  are done with a branch-and-cut algorithm based on polyhedral investigations of the atrix decomposition problem.  ...  We want to call this graph the conflict graph associated to the matrix decomposition problem (A,ß,K) and denote it by G c (A,ß). In formulas: G C (A,ß) -G(lP^t^).  ... 
doi:10.1137/s1052623497318682 fatcat:k2u6rq6vfzhz3m2tkegllpqfta

Detect Camouflaged Spam Content via StoneSkipping: Graph and Text Joint Embedding for Chinese Character Variation Representation [article]

Zhuoren Jiang, Zhe Gao, Guoxiu He, Yangyang Kang, Changlong Sun, Qiong Zhang, Luo Si, Xiaozhong Liu
2019 arXiv   pre-print
In particular, a Variation Family-enhanced Graph Embedding (VFGE) algorithm is designed based on a Chinese character variation graph.  ...  The VFGE can learn both the graph embeddings of the Chinese characters (local) and the latent variation families (global).  ...  Research Funds for the Central Universities (18lgpy62).  ... 
arXiv:1908.11561v1 fatcat:d3pjbpwqjzft3plnlrau2zefii

Detect Camouflaged Spam Content via StoneSkipping: Graph and Text Joint Embedding for Chinese Character Variation Representation

Zhuoren Jiang, Zhe Gao, Guoxiu He, Yangyang Kang, Changlong Sun, Qiong Zhang, Luo Si, Xiaozhong Liu
2019 Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP)  
In particular, a Variation Family-enhanced Graph Embedding (VFGE) algorithm is designed based on a Chinese character variation graph.  ...  The VFGE can learn both the graph embeddings of the Chinese characters (local) and the latent variation families (global).  ...  Graph vs. Text. Generally, the graph based baselines outperformed the textual based baselines (including general and Chinese).  ... 
doi:10.18653/v1/d19-1640 dblp:conf/emnlp/JiangGHKSZSL19 fatcat:yqij57cy35fh5gdcjy4u73sfxy

RANKING VALID TOPOLOGIES OF THE SECONDARY STRUCTURE ELEMENTS USING A CONSTRAINT GRAPH

KAMAL AL NASR, DESH RANJAN, MOHAMMAD ZUBAIR, JING HE
2011 Journal of Bioinformatics and Computational Biology  
We developed a directed weighted graph, the topology graph, to represent the secondary structure assignment problem.  ...  The largest protein in the test contains 18 helical sticks detected from the density map out of 33 helices in the protein.  ...  In this paper, we propose a general framework to the topology determination problem using a weighted directed graph.  ... 
doi:10.1142/s0219720011005604 pmid:21714133 fatcat:y4rzdxqcqbhzpcy42wes6n7umq

A Permutation-Based Differential Evolution Algorithm Incorporating Simulated Annealing for Multiprocessor Scheduling with Communication Delays [chapter]

Xiaohong Kong, Wenbo Xu, Jing Liu
2006 Lecture Notes in Computer Science  
In order to avoid the above problem, we combine differential evolution algorithm with simulated annealing algorithm which relaxes the criterion selecting the next generation.  ...  The results demonstrate that the hybrid differential evolution generates better solutions even optimal solutions in most cases and simultaneously meet scalability.  ...  In our experiments, we select the ogra100 problem with different edge densities , which is defined as the number of edges divided by the number of edges of a completely connected graph with the same number  ... 
doi:10.1007/11758501_70 fatcat:aajun3whwvbvzkkquam6hp3g3y

A learning automata-based memetic algorithm

M. Rezapoor Mirsaleh, M. R. Meybodi
2015 Genetic Programming and Evolvable Machines  
We used MGALA to solve two problems: object partitioning and graph isomorphism.  ...  In addition, in MGALA the learned traits are not passed to the offspring.  ...  cycles problem [19] , sorting problems in graphs [20] , the graph bandwidth minimization problem [21] [22] [23] , software clustering problems [24, 25] , the single machine total weighted tardiness  ... 
doi:10.1007/s10710-015-9241-9 fatcat:v6bx55o36neonl6n4vijp2x2ue

A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors

Abhishek Biswas, Dong Si, Kamal Al Nasr, Desh Ranjan, Mohammad Zubair, Jing He
2011 2011 IEEE International Conference on Bioinformatics and Biomedicine  
For clear viewing, only SSEs at the front of the structure are labeled.  ...  Due to the uncertainty in either source of information, a pool of possible secondary structure positions has to be sampled in order to include the true answer.  ...  The topology determination problem can be described as a problem to find a permutation Ȗ of ሼͳǡ ʹǡ ǥ ǡ ܰሽ such that assigning H i to ܵ ఊሺሻ ǡ ݅ ൌ ͳǡ ǥ ǡ ܰ minimize the assignment score.  ... 
doi:10.1109/bibm.2011.73 dblp:conf/bibm/BiswasSARZH11 fatcat:3isdkurzrjc2xbdipumoj56dva

Analytical Approaches to Improve Accuracy in Solving the Protein Topology Problem

Kamal Al Nasr, Feras Yousef, Ruba Jebril, Christopher Jones
2018 Molecules  
By treating the correspondence between the detected structures and the structures predicted from sequence data as a constraint graph problem DP-TOSS achieved good accuracy in its original iteration.  ...  It produces volumetric images (we refer to them as volumes in this paper) of the target molecule, generally at sub/nanometer (>5 Å) resolution.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules23020028 pmid:29360779 fatcat:da7oaep7mvgovmcrk75ps26p4a

Ant Colony Optimization Algorithm for Workforce Planning

Stefka Fidanova, Gabriel Luque, Olympia Roeva, Marcin Paprzycki, Paweł Gepner
2017 Proceedings of the 2017 Federated Conference on Computer Science and Information Systems  
The problem is to select set of employers from a set of available workers and to assign this staff to the jobs to be performed. Each job requires a time to be completed.  ...  The workforce planning helps organizations to optimize the production process with aim to minimize the assigning costs.  ...  and DFNI I02/20 "Efficient Parallel Algorithms for Large-Scale Computational Problems", and by the Polish-Bulgarian collaborative grant "Parallel and Distributed Computing Practices".  ... 
doi:10.15439/2017f63 dblp:conf/fedcsis/FidanovaLRPG17 fatcat:idygdh5b2ve5tfgnkmkdkvdrje

Hedonic Games with Fixed-Size Coalitions

Vittorio Bilò, Gianpiero Monaco, Luca Moscardelli
2022 PROCEEDINGS OF THE THIRTIETH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE AND THE TWENTY-EIGHTH INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE  
agent in the same coalition.  ...  In this work, we initiate the study of hedonic games with fixed-size coalitions, where the set of possible coalition structures is restricted as follows: there are k coalitions, each coalition has a fixed  ...  This problem is well posed, as we prove in Theorem 1 that stable assignments always exist for any X ∈ {SSS, SS, SSTU}.  ... 
doi:10.1609/aaai.v36i9.21156 fatcat:eqr7cumr4zgmfmur6nwievqomi

Almost Disjoint Paths and Separating by Forbidden Pairs [article]

Oliver Bachtler, Tim Bergner, Sven O. Krumke
2022 arXiv   pre-print
In this paper, we explore these two problems, showing that they have an unbounded duality gap in general and analyzing their complexity.  ...  The max-flow problem in a network with unit capacities is equivalent to the arc-disjoint paths problem. Moreover the max-flow and min-cut problems form a strongly dual pair.  ...  We analyze the complexity of the weakly dual problems ADP and SFP. In Section 2 we define these problems in addition to introducing notation and stating general assumptions.  ... 
arXiv:2202.10090v1 fatcat:asogjnvgdjg5rkhb446p2cjxwe
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